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Possible to call variants from PacBio reads from a mixed sample?
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2.3 years ago
nchuang • 200

For whatever reason my PI decided to submit many long amplicons for PacBio sequencing without barcoding each amplicon. He now wants to know how much variation exists between the samples. I was looking at the Long Amplicon Analysis (LAA) tool and it says it can generate consensus based on unique individual molecules. I don't know if it can account for each molecule without barcoding.

Is there a way to call variation on this mixed sample file? I already did a simple bam-readcount and it gives too many possible variants at each site. I figured I need a true variant caller to distinguish true variants. Samtools/Bcftools mpileup basically stalls out with nothing written to file. I am assuming it can't handle the long reads.

pacbio long reads SNP • 296 views

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